In vitro recombination method

ABSTRACT

The present invention relates, e.g., to in vitro method, using isolated protein reagents, for joining two double stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity, comprising contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5′ exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser.No. 15/385,537 filed Dec. 20, 2016, now issued as U.S. Pat. No.10,577,629; which is a continuation application of U.S. application Ser.No. 12/750,571 filed Mar. 30, 2010, now issued as U.S. Pat. No.9,534,251; which is a divisional application of U.S. application Ser.No. 11/502,746 filed Aug. 11, 2006, now issued as U.S. Pat. No.7,723,077; which claims the benefit under 35 USC § 119(e) to U.S.Application Ser. No. 60/707,160 filed Aug. 11, 2005, now expired. Thedisclosure of each of the prior applications is considered part of andis incorporated by reference in the disclosure of this application.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant numberDE-FG02-02ER63453 awarded by the U.S. Department of Energy. Thegovernment has certain rights in the invention.

BACKGROUND OF THE INVENTION Field of the Invention

This invention relates, e.g., to in vitro methods for joining(recombining) double stranded DNA molecules via a region of homology. Inone embodiment, a plurality of DNA molecules are joined into a longerDNA molecule in a predefined order and orientation.

Background Information

Homologous recombination of linear double stranded DNA has long beenknown to be crucial for the repair of double stranded DNA breaks. Inmost organisms, the initiation of homologous recombination requires theaction of an exodeoxyribonuclease. The single stranded DNA fragmentgenerated can then pair with homologous sequence on other DNA moleculesto complete the recombination. Although homologous recombination hasbeen intensely studied, the mechanism involved is still not fullyunderstood. The most efficient homologous recombination system has beendiscovered in Deinococcus radiodurans, which can survive 15,000 Gy ofionizing radiation, while doses below 10 Gy are lethal to almost allother organisms (Daly et al. (1996) J. of Bacteriology 178, 4461-4471).However, due to the complexity of the D. radiodurans genome, it isextremely difficult to pinpoint the proteins involved in the homologousrecombination process.

Homologous recombination has also been demonstrated in theenterobacteria phage T7 system, the efficiency of which can be more than50% (Lai et al. (1998) J. of Bacteriology 180, 6193-6202). T7 phagecontain only 56 genes which encode 59 proteins, and therefore would be amore suitable system to isolate proteins involved in homologousrecombination. In the T7 genome, genes that are involved in similarfunctions are normally clustered together. It has been reported that theearly genes from gene 1.3 ligase to gene 6 exonuclease may be importantin recombination (Lee et al. (1983) J. of Virology 48, 647-653; Lai etal. (1998), supra; Lai et al. (2000) Molecular Microbiology 36, 437-466;Yu et al. (2001) J. of Bacteriology 183, 1862-1869). However, it is notknown whether host proteins are also important in this process.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a cartoon illustrating a joining reaction of the invention.The joined molecules are shown as linear molecules; however, it is to beunderstood that the ends of the linear molecule are preferably joined toform a circle, and/or are joined to a linearized vector, to form acircle.

FIG. 2 is a cartoon illustrating a method for adding overlappingsequences by PCR amplification. As shown in the center panel, Fragment 1is PCR amplified, to add sequence A at the 3′ end. Fragment 2 is PCRamplified, to add sequence B to the 3′ end. The joined molecules areshown as linear molecules; however, it is to be understood that the endsof the linear molecule are preferably joined to form a circle, and/orare joined to a linearized vector, to form a circle.

FIG. 3 is a cartoon illustrating a method for inserting a fragment intoa vector.

FIG. 4 is a cartoon illustrating a method for adding overlappingsequences by PCR amplification.

FIG. 5 shows the results of incubating four DNA fragments by a method ofthe invention, for 20 minutes or 45 minutes. Lanes 1-4 show results fromincubation for 20 min, lanes 5-8 show results from incubation for 45 minat 30° C. The reaction for each lane started with 6 μg total DNA (4fragments of 2.2 kb, 1.5 kb, 1.55 kb and 1.2 kb), 30 U/ml T7 DNApolymerase, and 4000 U/ml T4 DNA ligase. Lanes 1-4 and 5-8 show resultsfrom reactions containing 20, 2, 4, 0.4 U/ml exonuclease and 1, 1.5, 2,2 μM T7 ssb, respectively.

FIG. 6 shows the results of incubating four DNA fragments by a method ofthe invention, for 60 minutes. Conditions were similar to those for lane2 and 6 of FIG. 5. Lane 1 shows results of a reaction with control DNAonly. Lanes 2 and 3 show results from duplicates, incubated at 30° C.for 60 minutes. Lane 4 shows results of a sample without ligase. Lane 5shows results from a sample without ssb.

DETAILED DESCRIPTION OF THE INVENTION

The present inventors have identified four T7 gene products (orsubstitutes therefor) that are sufficient to constitute an in vitrosystem for recombining DNAs via a region of homology. The method allows,e.g., for the joining of DNA molecules of interest to one another in apredefined order and orientation, without the use of restrictionenzymes.

The present invention relates, e.g., to an in vitro method, usingisolated protein reagents (proteins), for joining two double stranded(ds) DNA molecules of interest, wherein the distal region of the firstDNA molecule and the proximal region of the second DNA molecule share aregion of sequence identity, comprising contacting the two DNA moleculeswith

-   -   (a) a non-processive 5′ exonuclease;    -   (b) a single stranded DNA binding protein (SSB) which        accelerates nucleic acid annealing;    -   (c) a non strand-displacing DNA polymerase; and    -   (d) a ligase,        under conditions effective to join the two DNA molecules to form        a substantially intact (un-nicked) double stranded DNA molecule        in which a single copy of the region of sequence identity is        retained. In this method, the 5′ exonuclease generates 3′ single        stranded overhangs in both DNA molecules which comprise the        region of sequence identity; the two single stranded overhangs        anneal to form a gapped molecule; the DNA polymerase fills in        the gaps; and the ligase seals the nicks. The method is        illustrated schematically in FIG. 1.

The “joining” of two DNA molecules so that a single copy of the regionof sequence identity is retained is sometimes referred to herein as“recombination” of the two DNA molecules. In the method of theinvention, the four proteins (a) through (d) are each isolated (e.g.,purified); cell extracts are not employed. The four proteins acttogether in a concerted fashion; the individual enzymatic reactions arenot actively terminated (e.g., by an experimenter or investigator)before a subsequent reaction begins. In some embodiments, formation of adouble stranded DNA molecule results in the molecule being relativelywithdrawn or inert from the reactions. Conditions which are effectivefor joining the two DNA molecules allow for the net assembly of DNAmolecules, rather than the degradation of the DNA molecules by theexonuclease. That is, the gaps formed by digestion by the 5′ exonucleaseare filled in by the polymerase substantially immediately after they areformed. This is accomplished by contacting the DNA molecules with asubstantially lower amount of 5′ exonuclease activity than the amount ofDNA polymerase activity.

The method can be used to join more than two DNA molecules. Toaccomplish this, the DNA molecules to be joined are designed such that,for each pair of DNA molecules to be joined, the distal region of oneDNA molecule comprises a region of sequence identity with the proximalregion of the other DNA molecule. To facilitate the joining of the DNAmolecules in a predetermined orientation and order, each set of distaland proximal regions of sequence identity is selected (designed) to beunique (to be different from the regions of sequence identity of theother pairs of DNA molecules). The method allows a number of DNAmolecules to be joined with a single operation (e.g., in a single tube).See FIG. 1 for a schematic representation of such predetermined joining.

Advantages of the method of the invention include the ability to performthe joining (recombination) reactions under well-defined conditions,using well-characterized, isolated (e.g., purified) proteins (e.g.,enzymes). This allows the joining reactions to be controlled andreproducible. In the method of the invention, the joining process is notsubject to competing reactions brought about by other enzymes in thereaction mixture, such as exonucleases and endonucleases which can bepresent in cell extracts. The method allows one to recombine regions ofsequence identity (homologous regions) that are less than about 150 basepairs in length. This is in contrast, e.g., to recombination systemsusing cell lysates rather than isolated enzymes; in systems using celllysates, efficient joining does not occur with overlaps of less thanabout 150 bp. The ability to join DNA molecules in a defined order andorientation allows, for example, for the cloning of a fragment ofinterest into a linearized vector in a defined orientation; or for theassembly of component DNA portions of a longer sequence of interest(such as the assembly of component parts of a synthetic gene or genome;or the assembly and cloning of sub-fragments of a DNA which are toolarge to clone using a PCR amplification step). The method allows one tojoin and/or clone DNA molecules of interest without having to rely onthe presence of restriction enzyme recognition sites at the ends of thefragments to be joined. The in vitro procedure also allows one toassemble DNAs that are unstable and thus would be difficult to clone bya method requiring transformation into and replication in a bacterium.If desired, DNAs assembled by a method of the invention can then beamplified in vitro (e.g., by rolling circle amplification or PCR), againwithout having to passage the DNA through a bacterium.

One aspect of the invention is an in vitro joining method as above,wherein the 5′ exonuclease is the phage T7 gene 6 product, RedA oflambda phage, or RecE of Rac prophage; the SSB is the phage T7 gene 2.5product, the E. coli recA protein, RedB of lambda phage, or RecT of Racprophage; the DNA polymerase is the phage T7 gene 5 product, phage T4DNA polymerase, or E. coli pol I; and/or the ligase is the phage T7 gene1.3 product, phage T4 DNA ligase, or E. coli DNA ligase.

Another aspect of the invention is an in vitro method, using isolatedprotein reagents, for joining two double stranded (ds) DNA molecules ofinterest, wherein the distal region of the first DNA molecule and theproximal region of the second DNA molecule share a region of sequenceidentity, comprising generating 3′ single stranded (ss) overhangs atboth ends of the DNA molecules; annealing the single stranded overhangsin the presence of a ssDNA binding protein; filling in the gaps formed,and sealing the nicks.

Another aspect of the invention is a kit for the in vitro joining of aplurality of dsDNA molecules comprising, in separate containers,

-   -   (a) a mixture of the isolated proteins        -   (i) a single stranded DNA binding protein (SSB) which            accelerates nucleic acid annealing (e.g., the T7 gene 2.5            product, the E. coli recA protein, RedB of lambda phage, or            Rec T of Rac prophage);        -   (ii) a non strand-displacing DNA polymerase (e.g., the phage            T7 gene 5 product, phage T4 DNA polymerase, or E. coli pol            1); and        -   (iii) a DNA ligase (e.g., the phage T7 gene 1.3 product,            phage T4 DNA ligase, or E. coli DNA ligase),    -   wherein the ratios of activities of (i), (ii) and (iii) are        effective, when in the presence of a non-processive 5′        exonuclease, to achieve in vitro joining of the dsDNA molecules,        and    -   (b) an isolated 5′ exonuclease (e.g., the phage T7 gene 6        product, RedA of lambda phage, or RecE of Rac prophage).

Another aspect of the invention is a composition comprising

-   -   (a) an isolated 5′ exonuclease (e.g., the phage T7 gene 6        product, RedA of lambda phage, or RecE of Rac prophage);    -   (b) a single stranded DNA binding protein (SSB) which        accelerates nucleic acid annealing (e.g., the T7 gene 2.5        product, the E. coli recA protein, RedB of lambda phage, or Rec        T of Rac prophage);    -   (c) a non strand-displacing DNA polymerase (e.g., the phage T7        gene 5′ product, phage T4 DNA polymerase, or E. coli pol I); and    -   (d) a DNA ligase (e.g., the phage T7 gene 1.3 product, phage T4        DNA ligase, or E. coli DNA ligase).

Such a composition can be present, for example, in a reaction mixture inwhich a plurality of DNA molecules are being joined by a method of theinvention.

As used herein, the singular forms “a,” “an,” and “the” include pluralreferents unless the context clearly dictates otherwise. For example,“an” isolated exonuclease, as used above, includes two or moreexonuclease molecules, which can be the same or different.

The term, an “isolated” protein, as used herein, means that the proteinis removed from its original environment (e.g., the natural environmentif it is naturally occurring), and isolated or separated from at leastone other component with which it is naturally associated. For example,a naturally-occurring protein present in its natural living host (e.g.,a bacteriophage protein present in a bacterium that has been infectedwith the phage) is not isolated, but the same protein, separated fromsome or all of the coexisting materials in the natural system, isisolated. Such proteins can be part of a composition or reactionmixture, and still be isolated in that such composition or reactionmixture is not part of its natural environment. The term “an isolatedprotein,” as used herein, can include 1, 2, 3, 4 or more copies of theprotein, i.e., the protein can be in the form of a monomer, or it can bein the form of a multimer, such as dieter, trimer, tetramer or the like,depending on the particular protein under consideration. In someembodiments, the protein is purified. Methods for purifying the proteinsof the invention are conventional. In some embodiments, the protein issubstantially purified or is purified to homogeneity. By “substantiallypurified” is meant that the protein is separated and is essentially freefrom other proteins, i.e., the protein is the primary and activeconstituent. The purified protein can then be contacted with the DNAs tobe joined, where it then acts in concert with other proteins to achievethe joining. The proteins can be contacted with (combined with) the DNAsin any order; for example, the proteins can be added to a reactionmixture comprising the DNAs, or the DNAs can be added to a reactionmixture comprising the proteins. Proteins used in the methods of theinvention can be in the form of “active fragments,” rather than thefull-length proteins, provided that the fragments retain the activities(enzymatic activities or binding activities) required to achieve thejoining. One of skill in the art will recognize how to generate suchactive fragments.

Any non-processive 5′→3′ double strand specific exodeoxyribonuclease maybe used in the methods of the invention. The terms “5′ exonuclease” or“exonuclease” are sometimes used herein to refer to a 5′→3′exodeoxyribonuclease. A “non-processive” exonuclease, as used herein, isan exonuclease that degrades a limited number (e.g., only a few)nucleotides during each DNA binding event. Among other properties whichare desirable for the 5′ exonuclease are that it lacks 3′ exonucleaseactivity, it is double strand DNA specific, it generates 5′ phosphateends, and it initiates degradation from both 5′-phosphorylated andunphosphorylated ends. Suitable 5′ exonucleases will be evident to theskilled worker. Among the preferred 5′ exonucleases are the phage T7gene 6 product, RedA of lambda phage (lambda exonuclease), RecE of Racprophage, or any of a variety of 5′→3′ exonucleases that are involved inhomologous recombination reactions. Methods for preparing the T7 gene 6product and optimal reaction conditions for using it are conventional.See, e.g., Kerr et al. (1972) The Journal of Biological Chemistry 247,305-310. Methods for preparing and using the other noted exonucleasesare conventional; and many are available from commercial sources, suchas USB Corporation, 26111 Miles Road, Cleveland, Ohio 44128, or NewEngland Biolabs, Inc. (NEB), 240 County Road, Ipswich, MA 01938-2723.

Without wishing to be bound by any particular mechanism of action, it issuggested that a single stranded DNA binding protein (SSB) used in amethod of the invention protects the single stranded overhangs generatedby the 5′ exonuclease, as well as facilitating the rapid annealing ofthe homologous single stranded regions. Any SSB which acceleratesnucleic acid annealing may be used in a method of the invention. An SSBwhich “accelerates nucleic acid annealing,” as used herein, is an SSBwhich accelerates nucleic acid binding by a factor of greater than about500 fold, compared to the binding in the absence of the SSB. See, e.g.,U.S. Pat. No. 5,534,407. Among other properties which are desirable forthe SSB are that it binds single stranded DNA (ssDNA) more tightly thandouble stranded DNA (dsDNA), and that it interacts with both theexonuclease and the DNA polymerase. Suitable SSBs will be evident to theskilled worker. Among the preferred SSBs are the T7 gene 2.5 product,the E. coli RecA protein, RedB of lambda phage, and RecT of Racprophage. Methods for preparing the T7 protein and optimal reactionconditions for rising it are conventional. See, e.g., Rezende et al.(2002) Journal of Biological Chemistry 277, 50643-53 and Yu et al.(2001), supra. Methods for preparing and using the other SSBs areconventional; and many are available commercially, e.g., from USB orNEB, as noted above. In yet a further embodiment, polyethylene glycol(“PEG”) may be used to enhance the annealing process.

Any non strand-displacing DNA polymerase may be used in the methods ofthe invention to fill in the gaps left by the 5′ exonuclease digestion.The term “polymerase” is sometimes used herein to refer to a DNApolymerse. A “non strand-displacing DNA polymerase,” as used herein, isa DNA polymerase that terminates synthesis of DNA when it encounters DNAstrands which lie in its path as it proceeds to copy a dsDNA molecule,or degrades the encountered DNA strands as it proceeds while currentlywith filling in the gap thus created, thereby generating a “movingnick.” Among the other properties which are desirable for the nonstrand-displacing DNA polymerase are that it synthesizes DNA faster thanthe exonuclease in the reaction mixture degrades it. Suitable nonstrand-displacing DNA polymerases will be evident to the skilled worker.Among the preferred enzymes are the T7 gene 5 product, T4 DNA,polymerase, and E. coli Pol1. Methods for preparing and using theabove-noted DNA polymerases are conventional; and many are availablecommercially, e.g., from USB or NEB, as noted above.

Any DNA ligase can be used in the methods of the invention. The term“ligase” is sometimes used herein to refer to a DNA ligase. Suitable DNAligases include, e.g., the T7 gene 1.3 product, T4 DNA ligase, E. coliDNA ligase and Taq Ligase. Methods for their preparation and optimalreaction conditions are conventional. Alternatively, they can bepurchased from commercial sources, such as USB or NEB, as noted above.In a preferred embodiment, substantially all of the nicks (e.g., all ofthe nicks) are sealed during the reaction procedure, in order to preventdegradation by the exonuclease. However, in one embodiment, joined DNAwhich still comprises some nicks is transformed into a bacterium, suchas E. coli, and the nicks are sealed by the bacterial machinery.

The four proteins used in the methods of the invention (the exonuclease,SSB, polymerase and ligase) may be contacted with the DNA molecules tobe joined (e.g., added to a reaction mixture comprising a solutioncontaining suitable salts, buffers, ATP, deoxynucleotides, etc. plus theDNA molecules) in any order. In one embodiment, the four proteins areadded substantially simultaneously. For example, a mixture of the fourproteins in suitable ratios can be added to the reaction mixture with asingle pipetting operation. In other embodiments, the exonuclease isadded last; and preceding the addition of the exonuclease, the SSB,polymerase and ligase are added sequentially, in any order, or two ofthe proteins are added substantially simultaneously, and the otherprotein is added before or after those two proteins. In one embodiment,the proteins are added in the following order: SSB, ligase, polymerase,exonuclease. A skilled worker can readily optimize the timing of thecombination of the four individual proteins. In one embodiment, the fourproteins are rapidly, sequentially added to the DNAs, within about 1-2minutes of one another.

In another embodiment of the invention, the DNAs are added to a reactionmixture comprising a solution containing suitable salts, buffers, ATP,deoxynucleotides, etc. and the four proteins. In another embodiment, theDNAs are added to a reaction mixture comprising a solution containingsuitable salts, buffers, ATP, deoxynucleotides, etc. and a subset of thefour proteins, and the remaining proteins are then added, in any orderor in any combination (e.g., the exonuclease is added last; andpreceding the addition of the exonuclease, the SSB, polymerase andligase are added sequentially, in any order, or two of the proteins areadded substantially simultaneously, and the other protein is addedbefore or after those two proteins).

In the methods of the invention, a plurality of DNA molecules arecontacted with the four proteins under conditions “effective” to jointhe DNA molecules to form a substantially intact (preferably having nonicks) double stranded DNA molecule, in which a single copy of theregion of sequence identity is retained. An important factor inachieving the joining is that the amount of 5′ exonuclease activityshould be substantially lower than the amount of DNA polymeraseactivity, so that the net assembly of DNA molecules is greater than thedegradation of DNA molecules by the exonuclease. That is, the gapsformed by digestion by the 5′ exonuclease are filled in by thepolymerase substantially immediately after they are formed, and theintact (un-nicked) reaction product is “fixed” by the ligation reaction.Suitable amounts of activities include: exonuclease activity betweenabout 0.1 and about 50 U/mL (unit defined by USB); DNA polymerasebetween about 10 and about 30 U/mL (unit defined by USB); SSB betweenabout 0.1 and about 1 μM; and ligase between about 0.1 and about 1 μM.Lower amounts of polymerase would likely not able to catch up with theexonuclease, and higher amounts would likely degrade the 3′ overhanggenerated by exonuclease, resulting in overlaps being digested beforeannealing can occur. Lower amounts of SSB would likely not allowannealing to occur rapidly enough, and higher amounts would likelystimulate exonuclease processivity, also resulting in polymerase cannotcatch up. See Example I for some typical ratios that can be used.

Reaction conditions (such as the presence of salts, buffers, ATP, dNTPs,etc. and the times and temperature of incubation) are conventional andcan be optimized readily by one of skill in the art. Preferably, theincubation temperature is about 25° C. to about 45° C., and the reactionis carried out for about 1-1.5 hours at 37° C., or for about 2-3 hoursat 30° C. Typical reaction conditions are presented in Example I.

Because a non-strand displacing DNA polymerase used in the methods ofthe invention must elongate in the 5′ direction from a primer molecule,the method cannot tolerate a free 5′ end (e.g., at the 5′ end of themost 5′ DNA to be joined). Because no primer is available in such amolecule to be extended, such a molecule would be digested by theexonuclease and the resulting gap could not be filled in by apolymerase. In one embodiment, the 5′ ends of the terminal DNA fragmentsthat are joined are blocked so that 5′ exonuclease cannot digest them.The blocking agent is preferably reversible, so that the joined DNAmolecule can eventually be joined into a vector. Suitable blockingagents will be evident to the skilled worker. These include, e.g.,phosphorothioate bonds, 5′ spacer molecules, Locked Nucleic Acid (LNA)etc. In another embodiment of the invention, the fragments are selected(designed) so that the two terminal fragments join to one another toform a circle. In another embodiment, the joined fragments are designedso that they become integrated into a vector which is also present inthe reaction mixture.

DNA molecules of any length can be joined by methods of the invention,and from two to an essentially unlimited upper level of DNA moleculescan be joined. In general, at least about 10 fragments can be joined.The number of fragments which can be joined depends, e.g., on the lengthof the overlaps and the lengths of the fragments. For example, withfragments of greater than about 3 kb, having overhangs of about 150 toabout 200 bp, the number of fragments that can be joined issubstantially unlimited.

As noted above, in embodiments of the invention in which no blocker isused, the joined DNA molecules preferably form a circle and/or becomeligated into a vector to form a circle. The lower size limit for a dsDNAto circularize is about 200 base pairs. Therefore, the total length ofthe joined fragments (including, in some cases, the length of thevector) is preferably at least about 200 by in length. There is no uppersize limit, and joined DNAs of a few hundred kilobase pairs, or larger,can be generated by a method of the invention. Although the rate atwhich the circles can form may be reduced for very long molecules, thatdoes not prevent the circle from forming and reaching a steady state inwhich the rate of filling in gaps is greater than the rate ofexonuclease digestion, once all of the nicks have been sealed. Example Iillustrates joining/recombination reactions in which four DNA molecules,of 2.2 kb, 1.5 kb, 1.55 kb and 1.2 kb, are joined.

In methods of the invention, the distal region of one of a pair of dsDNAmolecules to be joined shares a region of sequence identity with theproximal region of the other dsDNA molecule. The term “distal” as usedherein refers to the 3′ end of a first DNA molecule of a pair to bejoined (the 5′-most DNA molecule), and the term “proximal” refers to the5′ end of the second DNA molecule of the pair. The regions of identityare sometimes referred to herein as “overlaps” or “regions of overlap.”FIG. 1 shows a schematic representation of the distal and proximalregions of DNA molecules to be joined. The region of sequence identityshould be sufficiently long to allow the recombination to occur. Thelength can vary from a minimum of about 15 base pairs (bp) to a maximumof about 300 by or more. In general, it is preferable that the length ofthe overlap is not greater than about 1/10 the length of the fragment tobe recombined; otherwise there may not be sufficient time for annealingand gap filling. For the joining of 2 or 3 fragments, about 20-30 byoverlap may be sufficient. For more than 10 fragments, a preferredoverlap is about 150 by to about 300 bp. If longer overlaps are used,the T7 endonuclease may also be required to debranch the jointmolecules. In one embodiment, the region of sequence identity is of alength that allows it to be generated readily by synthetic methods,e.g., about 40 by (e.g., about 35 to about 45 bp).

In a preferred embodiment, when a plurality of DNA molecules are to bejoined, for each pair of DNA molecules to be joined, the distal regionof one of the DNA molecules of the pair is designed to share a region ofsequence identity with the proximal region of the other DNA molecule ofthe pair, and the distal and proximal regions of sequence identity foreach pair of DNA molecules are designed to be unique (to be differentfrom the regions of sequence identity of the other pairs of DNAmolecules). When the overlapping regions of identity are designed inthis manner, the orientation and order of the DNA molecules in thejoined molecule can be predetermined. A number of DNA molecules (forexample, 4 or 6 molecules) can thus be incubated together in a singlereaction mixture (in a single vessel or container) with the fourproteins of the invention, and be joined into a longer DNA molecule inwhich the individual DNAs are arranged in any desired order andorientation.

The regions of sequence identity present in the proximal and distalregions of the DNAs to be joined can be generated by any of a variety ofmethods.

For example, in one embodiment of the invention, synthetically preparedfragments of a gene or genome of interest (e.g., about 5 kb in length)are optionally amplified (e.g., by PCR or by a rolling circle mechanism)and are joined by a method of the invention in the order and orientationin which they are located in the gene or genome. This procedure allowsthe preparation of a synthetic gene or genome. In this method, the firstDNA fragment (e.g., in the 5′ most portion of the gene or genome) issynthesized so that the region at its 3′ end (the distal end) contains asequence (e.g., about 40 bp) that is identical to the sequence at the 5′end (the proximal end) of the DNA fragment to which it is to be joined.The second DNA fragment, in turn, is synthesized so that it has, at itsdistal end, a sequence which is identical to the sequence at theproximal end of the third DNA fragment, and so on.

In other embodiments of the invention, the regions of identity areintroduced by PCR amplification.

In one such method, as illustrated in FIG. 3, a fragment of interest isinserted into a vector. For example, a plasmid vector can be linearizedwith a restriction enzyme, generating a sequence A (e.g., having 40 bp)to the left of the restriction enzyme cut and a sequence B (e.g., having40 bp) to the right of the restriction enzyme cut. The fragment to becloned into the vector is PCR amplified, using PCR primers which willintroduce sequence A at the left end of the fragment, and sequence B atthe right end of the fragment. The regions of sequence identity (in thisexample, each having 40 bp) allow the fragment to be joined to thevector in a desired orientation, to form a circular molecule.Alternatively, particularly when it is desirable to avoid errors whichmight be introduced into an insert during PCR amplification, the vectorcan be PCR amplified in order to introduce at the ends of a cloning sitesequences which overlap sequences at the ends of the insert. The methoddescribed above allows for the directional cloning of any insert ofinterest, without having to rely on the presence of, or introduction of,restriction enzyme sites on the insert.

In another such method, as illustrated in FIG. 2, a plurality of DNAfragments are joined to one another. In this embodiment, the regions ofsequence identity are introduced into the fragments by PCRamplification, using suitable primers, For each DNA fragment to bejoined to another fragment, a sequence is introduced to the 3′ (distal)end of the first fragment which overlaps with the sequence at the 5′(proximal) end of the fragment to which it is to be joined. PCR primersare used in which the regions of sequence identity (e.g., 40 nt) lie 5′to a PCR primer (e.g., having 20 nt). As shown in FIG. 2, after asuitable number of rounds of PCR amplification, DNA fragments areproduced in which defined regions of sequence identity are present atthe ends of the fragments. The resulting fragments can then be joined ina predetermined order and orientation by a method of the invention. Avariant of this method is shown in FIG. 4. In this method, starting withtwo representative fragments having no regions of sequence identity attheir ends, sequences are added by PCR amplification by primers havingonly 40 nt (instead of 60 nt); the resulting regions of sequenceidentity are 40 by in length. In FIGS. 1-3, the joined molecules areshown as linear molecules. As discussed above, the fragments at eitherend of a linear molecule are preferably joined to form a circle, and/orare joined to a linearized vector, to form a circle.

If desired, a vector can be present in the joining reaction, so that thejoined fragments are introduced into the vector. The efficiency of joining a large number of fragments (e.g., 6 or 8 fragments) into avector by a method of the invention is more efficient than when using amethod which employs compatible restriction enzyme sites. To increasethe efficiency even further, the DNAs from a joining reaction can beseparated by size (e.g., by gel electrophoresis or a sizing column); anda DNA molecule of the desired size (having the correct number of joinedfragments) can be isolated and introduced into a vector by a method ofthe invention.

In one embodiment, joined fragments and/or fragments inserted intovectors are introduced into a host cell, such as a bacterial oreukaryotic cell (e.g., by transfection or transformation).Alternatively, the reaction mixture comprising the joined DNA moleculescan be introduced into a host cell; only those DNAs which haverecombined to form circular molecules can survive in the host cell. Inanother embodiment, the joined fragments and/or fragments inserted intovectors are used directly, without further passage through a cell, suchas a bacterial cell.

Molecular biology methods of the invention can be carried out usingconventional procedures. See, e.g., discussions in Sambrook, et al.(1989), Molecular Cloning, a Laboratory Manual, Cold Harbor LaboratoryPress, Cold Spring Harbor, N.Y.; Ausubel et al. (1995), CurrentProtocols in Molecular Biology, N.Y., John Wiley & Sons; Davis et al.(1986), Basic Methods in Molecular Biology, Elseveir SciencesPublishing, Inc., New York; Hames et al. (1985), Nucleic AcidHybridization, IL Press; Dracopoli et al. (current edition) CurrentProtocols in Human Genetics, John Wiley & Sons, Inc.; and Coligan et al.(current edition) Current Protocols in Protein Science, John Wiley &Sons, Inc.

A variety of other uses for the inventive method will be evident to theskilled worker. In particular, the inventive method can be substitutedfor any method in which restriction enzyme digests are used to generatecompatible sequences for joining DNA molecules. In one embodiment of theinvention, DNA molecules that are too large to be amplified by PCR canbe cloned by joining sub-fragments by a method of the invention and theninserting them into a suitable vector. An in vitro recombination systemof the invention (e.g., the four proteins of the invention, in asuitable ratio) can be used to recombine any homologous DNAs ofinterest, e.g., to repair double stranded DNA breaks or gaps, etc.Another application of the method is to introduce a mutation into a DNA.In this method, a mutation is introduced into both the upper and lowerstrand PCR primers, so the amplified fragments are 100 mutant; then thefragments are joined by the method of the invention.

The disclosed methods can be used to join any nucleic acid molecules ofinterest. The nucleic acid molecules can come from any source, includinga cellular or tissue nucleic acid sample, cloned fragments or subclonesthereof, chemically synthesized nucleic acids, genomic nucleic acidsamples, cDNAs, nucleic acid molecules obtained from nucleic acidlibraries, etc. The DNAs can be radioactively labeled or can comprisebinding entities, such a biotinylated nucleotides, which can aid in thepurification of the joined DNAs. If desired, the DNA molecules to bejoined, or primers for adding overlapping regions of sequence identity,can be prepared synthetically. Conventional synthesis techniques includeusing phosphoroamidite solid-phase chemistry to join nucleotides byphosphodiester linkages. Chemistry for joining nucleotides byphosphorothioate linkages or different linkages, such asmethylphosphonate linkages, can also be used. For example, thecyanoethyl phosphoramidite method can be used, employing a Milligen orBeckman System 1 Plus DNA synthesizer (for example, Model 8700 automatedsynthesizer of Milligen-Biosearch, Burlington, Mass. or ABI Model 380B).Synthetic methods useful for making DNA molecules are also described byIkuta et al. (1984) Ann Rev. Biochem. 53, 323-356, (phosphotriester andphosphite-triester methods), and Narang et al. (1980) Methods Enzymol.65, 610-620 (phosphotriester method). DNAs prepared by methods as aboveare available from commercial sources, such as Integrated DNATechnologies (IDT), Coralville, Iowa.

Methods of the invention can be earned out in a high throughput fashion,using automated (e.g., robotic) systems, which allow many DNA joiningreactions to be carried out simultaneously.

Any combination of the materials useful in the disclosed methods can bepackaged together as a kit for performing any of the disclosed methods.For example, the four proteins: a non-processive 5′ exonuclease (e.g.,the phage T7 gene 6 product); a single stranded DNA binding protein(SSB) which accelerates nucleic acid annealing (e.g., the T7 gene 2.5product or the E. coli recA protein); a non strand-displacing DNApolymerase (e.g., the T7 gene 5 product, T4 DNA polymerase, and E. colipol I); and a ligase (e.g., T4 DNA ligase or E. coli DNA ligase) can bepackaged individually or in various combinations. In one embodiment, thefour proteins are packaged together in a single container (such as anEppendorf tube). In another embodiment, the exonuclease is packagedseparately, so that this enzyme can be added last to a reaction mixturecontaining the DNA molecules to be joined and the other three proteins.In a preferred embodiment, the SSB, polymerase and ligase are packagedtogether in suitable ratios so that an aliquot can be removed and addedto a reaction mixture containing DNAs so that, following the addition ofan exonuclease, DNA joining takes place. If desired, the proteinreagents can be packaged in single use form, suitable for carrying oneset of DNA joining reactions.

Optionally, kits of the invention comprise instructions for performingthe method. Other optional elements of a kit of the invention includesuitable buffers, packaging materials, etc. The protein reagents of thekit may be in containers in which they are stable, e.g., in lyophilizedform or as stabilized liquids. Preferably, the proteins are stored assolutions in 50% glycerol.

DNAs used in methods of the invention can have one or more modifiednucleotides. For example, they may contain one or more modifications toeither the base, sugar, or phosphate moieties. Modifications to the basemoiety would include natural and synthetic modifications of A, C, G, andT as well as different purine or pyrimidine bases, such as uracil-5-yl,hypoxanthin-9-yl (1), and 2-aminoadenin-9-yl. A modified base includesbut is not limited to 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and otheralkyl derivatives of adenine and guanine, 2-propyl and other alkylderivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil andcytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil),4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl andother 8-substituted adenines and guanines, 5-halo particularly 5-bromo,5-trifluoromethyl and other 5-substituted uracils and cytosines,7-methylguanine and 7-methyl adenine, 8-azaguanine and 8-azaadenine,7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.Additional base modifications can be found for example in U.S. Pat. No.3,687,808, Englisch et al. (1991) Angewandte Chemie, InternationalEdition 30, 613, and Sanghvi, Y. S., Chapter 15, Anti sense Research andApplications, pages 289-302, Crooke, S. T. and Lebleu, B. ed., CRCPress, 1993. Certain nucleotide analogs, such as 5-substitutedpyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines,including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.5-methylcytosine can increase the stability of duplex formation. Basemodifications often can be combined with for example a sugarmodification, such as 2′-O-methoxyethyl, to achieve unique propertiessuch as increased duplex stability. There are numerous United Statespatents such as U.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066;5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908;5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091;5,614,617; and 5,681,941, which detail and describe a range of basemodifications.

Nucleotide analogs can also include modifications of the sugar moiety.Modifications to the sugar moiety would include natural modifications ofthe ribose and deoxyribose as well as synthetic modifications. Sugarmodifications include but are not limited to the following modificationsat the 2′ position: OH; F; O—, S—, or N-alkyl; O—, S—, or N-alkenyl; O—,S— or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl andalkynyl may be substituted or unsubstituted C1 to C10, alkyl or C2 toC10 alkenyl and alkynyl. 2′ sugar modifications also include but are notlimited to —O[(CH₂)nO]nOCH₃, —O(CH₂)nOCH₃, —O(CH₂)nNH₂, —O(CH₂)nCH₃,—O(CH₂)n-ONH₂, and —O(CH₂)nONRCH₂)nCH₃)[₂, where n and m are from 1 toabout 10.

Other modifications at the 2′ position include but are not limited to:C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl,O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃,SO₂, CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl,aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleavinggroup, a reporter group, an intercalator, a group for improving thepharmacokinetic properties of an oligonucleotide, or a group forimproving the pharmacodynamic properties of an oligonucleotide, andother substituents having similar properties. Similar modifications mayalso be made at other positions on the sugar, particularly the 3′position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linkedoligonucleotides and the 5′ position of 5′ terminal nucleotide. Modifiedsugars would also include those that contain modifications at thebridging ring oxygen, such as CH2 and S. Nucleotide sugar analogs mayalso have sugar mimetics such as cyclobutyl moieties in place of thepentofuranosyl sugar. There are numerous United States patents thatteach the preparation of such modified sugar structures such as U.S.Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878;5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427;5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265;5,658,873; 5,670,633; and 5,700,920, each of which is hereinincorporated by reference in its entirety.

Nucleotide analogs can also be modified at the phosphate moiety.Modified phosphate moieties include but are not limited to those thatcan be modified so that the linkage between two nucleotides contains aphosphorothioate, chiral phosphorothioate, phosphorodithioate,phosphotriester, aminoalkylphosphotriester, methyl and other alkylphosphonates including 3,-alkylene phosphonate and chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates. It is understood that these phosphate or modifiedphosphate linkages between two nucleotides can be through a 3′-5′linkage or a 2′-5′ linkage, and the linkage can contain invertedpolarity such as 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixedsalts and free acid forms are also included. Numerous United Statespatents teach how to make and use nucleotides containing modifiedphosphates and include but are not limited to, U.S. Pat. Nos. 3,687,808;4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423;5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939;5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821;5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050.

It is understood that nucleotide analogs need only contain a singlemodification, but may also contain multiple modifications within one ofthe moieties or between different moieties.

Nucleotide substitutes are nucleotides or nucleotide analogs that havehad the phosphate moiety and/or sugar moieties replaced. Nucleotidesubstitutes include molecules having similar functional properties tonucleotides, but which do not contain a phosphate moiety, such aspeptide nucleic acid (PNA). Nucleotide substitutes include moleculesthat will recognize and hybridize to complementary nucleic acids in aWatson-Crick or Hoogsteen manner, but which are linked together througha moiety other than a phosphate moiety. Nucleotide substitutes are ableto conform to a double helix type structure when interacting with tireappropriate target nucleic acid.

Substitutes for the phosphate can be for example, short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These includethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH₂ component parts. Numerous United States patents disclosehow to make and use these types of phosphate replacements and includebut are not limited to U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444;5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938;5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225;5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289;5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439.

It is also understood in a nucleotide substitute that both the sugar andthe phosphate moieties of the nucleotide can be replaced, by for examplean amide type linkage (aminoethylglycine) (PNA). U.S. Pat. Nos.5,539,082; 5,714,331; and 5,719,262 teach how to make and use PNAmolecules. See also Nielsen et al. (1991) Science 254, 1497-1500.

DNA molecules of the invention can be made up of different types ofnucleotides or the same type of nucleotides. For example, one or more ofthe nucleotides in a primer can be ribonucleotides, 2′-O-methylribonucleotides, or a mixture of ribonucleotides and 2′-O-methylribonucleotides; about 10% to about 50% of the nucleotides can beribonucleotides, 2′-O-methyl ribonucleotides, or a mixture ofribonucleotides and 2′-O-methyl ribonucleotides; about 50% or more ofthe nucleotides can be ribonucleotides, 2′-O-methyl ribonucleotides, ora mixture of ribonucleotides and 2′-O-methyl ribonucleotides; or all ofthe nucleotides are ribonucleotides, 2′-O-methyl ribonucleotides, or amixture of ribonucleotides and 2′-O-methyl ribonucleotides. Thenucleotides can be comprised of bases (that is, the base portion of thenucleotide) and can comprise different types of bases. For example, oneor more of the bases can be universal bases, such as 3-nitropyrrole or5-nitroindole; about 10% to about 50% of the bases can be universalbases; about 50% or more of the bases can be universal bases; or all ofthe bases can be universal bases.

In the foregoing and in the following example, all temperatures are setforth in uncorrected degrees Celsius; and, unless otherwise indicated,all parts and percentages are by weight.

EXAMPLES Example 1

Four DNA molecules, having lengths of 2.2 kb, 1.5 kb, 1.55 kb and 1.2kb, were incubated according to a method of the invention, under theconditions noted in FIGS. 5 and 6. The reaction mixes were subjected togel electrophoresis, along with molecular weight markers. When thesamples were incubated for 45 minutes or 60 minutes, a major band ofabout 6.3 kb formed. This is the size expected for a joined productcontaining one copy of each of the DNAs.

Example 2

4 enzymes (T7 5′-exonuclease, Taq polymerase, VENT polymerase, and Taqligase) plus two or more overlapping DNA fragments which can form acircular DNA molecule when recombined, are recombined in a singlereaction mixture such that the final product is a circular moleculecontaining the recombined fragments.

T7 5′-exonucicase is used to chew-back the 5′-ends of the duplex DNAfragments, thus exposing the overlapping regions. This enzyme has noactivity on 3′-ends. It acts at free ends and at nicks in the DNA. Oncethe overlaps are exposed, they can anneal to form joints that can berepaired because the 3′-ends of the annealed regions can be extended bythe Taq polymerase, which prior to the exposure and annealing of theoverlaps was inactive in the reaction mixture. The purpose of the VENTpolymerase, which is in very low amount, is to remove any single3′nucleotide additions that are produced by the Taq polymerase on theDNA fragments ends prior to the action of the T7 exonuclease. When theextending 3′ends catch up to the 5′-ends, the Taq ligase completes therepair by ligating the 5′-3′ nick. The repaired joint is then resistantto further reaction by the enzymes. When the fragments are joined into acomplete circle, that product is resistant to further reaction and isthe desired end product of the reaction.

Annealing of the overlapping ends is accelerated by carrying out thereaction at elevated temperature (e.g., 45 to 60° C.) in the presence of5% PEG 8000 in the reaction buffer.

For an efficient reaction the enzymes must be balanced in amount so thatthe T7 degradation is somewhat slower than the rate of annealing,polymerization, and ligation. Taq ligase should be in large excess sothat repair is completed as soon as the polymerization fills in the gapscreated when the overlapping ends anneal with each other.

A suitable buffer for the reaction contains 20 mM Tris acetate, 50 mMpotassium acetate, 10 mM magnesium chloride, 5 mM DTT, 25 ug per ml BSA,5% PEG-8000, 200 uM dNTP's, 1 mM NAD, 0.1% Triton X-100, adjusted to pH7.9.

From the foregoing description, one skilled in the art can easilyascertain the essential characteristics of this invention, and withoutdeparting from the spirit and scope thereof, can make changes andmodifications of the invention to adapt it to various usage andconditions.

Without further elaboration, it is believed that one skilled in the artcan, using the preceding description, utilize the present invention toits fullest extent. The preceding preferred specific embodiments are,therefore, to be construed as merely illustrative, and not limitative ofthe remainder of the disclosure in any way whatsoever.

The entire disclosure of all applications, patents and publicationscited above and in the figures are hereby incorporated by reference.

What is claimed is:
 1. An in vitro method, using isolated proteins, forjoining two double strand (ds) DNA molecules of interest, comprising:providing a first dsDNA molecule and a second dsDNA molecule which sharea region of sequence identity at a terminal end on each DNA molecule;and contacting the two dsDNA molecules with: (a) a purified 5′exonuclease; (b) a purified DNA polymerase; and (c) a purified ligase,under conditions whereby: a 3′ single-stranded overhang is generated ineach molecule by the exonuclease without the use of a restrictionenzyme; the two single-stranded overhangs anneal to form a gappedmolecule; the gaps are filled in by the polymerase; and nicks are sealedby the ligase, thereby joining the molecules and forming a substantiallyintact double stranded DNA molecule, in which a single copy of theregion of sequence identity is retained, wherein none of the enzymaticreactions is actively terminated prior to beginning another of thereactions.
 2. The method of claim 1, wherein the 3′ single strandedoverhangs comprise the region of sequence identity.
 3. The method ofclaim 1, wherein the proteins of (a), (b), and (c) are contactedsimultaneously with the DNA molecules.
 4. The method of claim 1, whereinthe proteins of (b) and (c) are contacted simultaneously orsequentially, in any order, with the DNA molecules, and the protein of(a) is contacted last.
 5. The method of claim 1, wherein the proteinsare contacted with the DNA molecules sequentially, in the followingorder: (b), (c), and (a).
 6. The method of claim 1, wherein theexonuclease activity is substantially lower than the activity of the DNApolymerase, such that the gaps are filled in by the polymeraseimmediately as they are formed.
 7. The method of claim 1, wherein (a)the 5′ exonuclease is the phage T7 gene 6 product, RedA of lambda phage,or RecE of Rac prophage; (b) the DNA polymerase is the phage T7 gene 5product, phage T4 DNA polymerase, or E coli pol I; and/or (c) the ligaseis the phage T7 gene 1.3 product, phage T4 DNA ligase, or E coli DNAligase.
 8. The method of claim 1, wherein the three proteins of (a),(b), and (c), function in a concerted manner.
 9. The method of claim 1,wherein one or more of the DNA molecules to be joined are generatedsynthetically.
 10. The method of claim 9, wherein the DNA molecules tobe joined comprise adjacent portions of a gene or genome of interest andare synthesized so as to comprise overlapping regions of sequenceidentity at their ends; and the joining reaction joins the DNA moleculesto form part or all of a synthetic gene or genome.
 11. The method ofclaim 1, wherein the regions of sequence identity are added to the DNAmolecules to be joined by PCR amplification.
 12. The method of claim 1,further comprising subjecting the joined DNA molecules to a sizingprocedure, isolating DNA molecules of a desired length, and introducingthe isolated DNA molecules into a cell of interest.
 13. The method ofclaim 1, which is a method for inserting a DNA fragment of interest intoa linearized vector to form a circular molecule, further comprisingadding sequences by PCR amplification to each end of the substantiallyintact double-stranded DNA molecule, which sequences added by PCRamplification are identical to sequences on either end of the linearizedvector.
 14. The method of claim 1, wherein the region of sequenceidentity is about 40 base pairs in length.
 15. The method of claim 1,wherein the proteins of (a), (b), and (c) are contacted with the DNAmolecules in a single reaction vessel.
 16. The method of claim 1,wherein the 5′ exonuclease is the phage T7 gene 6 product, RedA oflambda phage, or RecE of Rac prophage.
 17. The method of claim 1,wherein the 5′ exonuclease is the T7 gene 6 product.
 18. An in vitromethod for joining a plurality of double stranded DNA molecules in adefined orientation and order, comprising: (a) selecting the DNAmolecules such that, for each pair of molecules to be joined, the distalregion of one DNA molecule comprises a region of sequence identity tothe proximal region of the other DNA molecule, and each set of distaland proximal regions of identity is unique for each pair of DNAmolecules to be joined; and (b) contacting the DNA molecules in areaction mixture with (i) a non-processive 5′ exonuclease; (ii) a singlestranded DNA binding protein (SSB) which accelerates nucleic acid; (iii)a non strand-displacing DNA polymerase; and (iv) a ligase, underconditions effective to join each pair of DNA molecules to form asubstantially intact duplex DNA molecule in which the region of sequenceidentity is retained.
 19. An in vitro method, using isolated proteinreagents, for joining a plurality of double strand (ds) DNA molecules ofinterest, wherein for each pair of molecules to be joined, the distalregion of one DNA molecule comprises a region of sequence identity tothe proximal region of the other DNA molecule, and each set of distaland proximal regions of identity is unique for each pair of DNAmolecules to be joined, comprising generating 3′ single strand overhangsat both ends of the DNA molecules; annealing the regions of sequenceidentity in the single stranded overhangs, in the presence of a ssDNAbinding protein, filling in the gaps formed; and sealing the nicks.